Multiple platform build/check report for BioC 3.22 - BUILD results for biodbUniprot on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for biodbUniprot on kjohnson3

To the developers/maintainers of the biodbUniprot package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbUniprot.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbUniprot

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot

StartedAt: 2025-10-30 15:46:34 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 15:46:39 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 5.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot
###
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* checking for file ‘biodbUniprot/DESCRIPTION’ ... OK
* preparing ‘biodbUniprot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbUniprot.Rmd’ using rmarkdown
INFO  [15:46:38.228] Loading definitions from package biodb version 1.18.0.
INFO  [15:46:38.936] Loading definitions from package biodbChebi version 1.16.0.
INFO  [15:46:38.946] Loading definitions from package biodbHmdb version 1.16.0.
INFO  [15:46:38.957] Loading definitions from package biodbNcbi version 1.14.0.
INFO  [15:46:38.966] Loading definitions from package biodbNci version 1.14.0.
INFO  [15:46:38.969] Loading definitions from package biodbUniprot version 1.16.0.
INFO  [15:46:39.056] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/uniprot-958d776f924f3e7a3bae586fa731b40c.

Quitting from biodbUniprot.Rmd:67-69 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbUniprot.Rmd' failed with diagnostics:
`chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
--- failed re-building ‘biodbUniprot.Rmd’

SUMMARY: processing the following file failed:
  ‘biodbUniprot.Rmd’

Error: Vignette re-building failed.
Execution halted